Orione, a web-based framework for NGS analysis in microbiology

Abstract

Summary: End-to-end next-generation sequencing microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult owing to a lack of interoperability, reproducibility and transparency. To overcome these limitations we present Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics.Availability and implementation: Orione is available online at http://orione.crs4.it.Contact: gianmauro.cuccuru@crs4.itSupplementary information: Supplementary data are available at Bioinformatics online.

Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing

“…250 bp (basepair) paired-end sequencing was performed using the Illumina MiSeq platform. Read quality metrics was evaluated using the FASTX-toolkit and de novo assembly was performed using the SPAdes 3.0.0 assembler implemented on the Orione Galaxy web server (http://orione.crs4.it/) [15,16]. K values were set to 21, 33, 55, 77, 99, and 127 as suggested in the SPAdes 3.0 manual.…”

Rare Detection of the Acinetobacter Class D Carbapenemase bla OXA-23 Gene in Proteus mirabilis

“…The isolate had no extended-spectrum ␤-lactamase (ESBL) or transferable AmpC ␤-lactamases that could have caused this (PCR negative for CTX-M, TEM, SHV, CIT, DHA, MOX, FOX, ACC, and EBC), and wild-type susceptibility to third-generation cephalosporins is not typically seen in strains Using primers designed in house, a number of PCR assays and Sanger sequencing were used to confirm and extend the genetic environment of bla and to fill in gaps between the involved contigs (8) (see Table S1 in the supplemental material). The bla OXA-23 -containing region was analyzed using Geneious 7.1 software (Biomatters Ltd., Auckland, New Zealand) and annotated with Prokka version 1.4.0 (9), which is included in Galaxy/CRS4 (Orione) (10). The OXA-23 gene was located downstream of an ISAba1-like insertion sequence element, resembling the structure of transposon Tn2008, although not surrounded by a classic 9-bp target site duplication (Fig.…”

Epithelial Coculture and l -Lactate Promote Growth of Helicobacter cinaedi under H 2 -Free Aerobic Conditions

“…The library was subjected to 50-bp paired-end sequencing on the Illumina HiSeq 2000 instrument at the Vanderbilt University genomics core facility (Vanderbilt Technologies for Advanced Genomics). Reads were aligned to the organism's genome (35) and quantified (total read counts and RPKM [reads per kilobase transcript per million reads] values) with the EDGE-pro software package (37), accessed online via the Orione Galaxy Server (38). For each biologic replicate, 18.9 to 25.8 million aligned reads were obtained.…”